-osformat strangeness

[Gary Williams, Tel 01223 494522]

Peter Rice wrote:
> 
> Gary Williams writes:
> 
> >Can anyone explain this behaviour? When I use '-osf staden' or '-osf
> >gcg' I get no output but no error messages.
> 
> Strictly, this happens when '-ossingle' is on. This forces output to
> go to a separate file for each sequence, and is turned on for formats
> that do not support multiple sequences in one file (GCG/GCG8,
> STADEN/EXPERIMENT, RAW/TEXT/PLAIN)
> 
> Any other format with -ossingle on the command line will do the same.
> 
> GCG and STADEN with -noossingle will write to the same file. For GCG
> format EMBOSS is able to read the resulting file (but GCG cannot :-)
> 
> This behaviour could be changed, but needs some careful planning.  For
> example, with one output file you may want it to be used. With many
> output files you may want them all to be automatically named.
> 
> Perhaps some special processing for stdout and stderr would be useful,
> and for user-defined output filenames the user's choice could at least
> be used for the first sequence (maybe with a warning for the second
> sequence if there is one).

This sounds more what I might expect.

> So many cases to consider. All packages that write GCG format face
> these kinds of problems.

Hmm I see what you mean, '-ossingle' toggles this behaviour with any
format, eg embl. It doesn't seem the right behaviour though. I guess
that whatever behaviour it is set up to have we will meet discrepencies
between what was expected and what is possible.

I still don't see why there should be a difference between using
'staden::outfile' and '-osf staden' though. Is this the expected
behaviour. If so why?:




tellurium<116>seqret embl:hsfau jjj.seq
Reads and writes (returns) sequences

tellurium<117>ls -l jjj.seq
-rw-r-----   1 gwilliam cs            560 Aug 10 16:06 jjj.seq

[Behaves as I expected]

tellurium<118>rm jjj.seq

tellurium<119>seqret embl:hsfau staden::jjj.seq
Reads and writes (returns) sequences

tellurium<120>ls -l jjj.seq
-rw-r-----   1 gwilliam cs            539 Aug 10 16:06 jjj.seq

[Behaves as I expected]

tellurium<122>rm jjj.seq

tellurium<123>rm hsfau.staden

tellurium<124>seqret embl:hsfau jjj.seq -osf staden
Reads and writes (returns) sequences

tellurium<125>ty jjj.seq
jjj.seq: No such file or directory

tellurium<126>ls -l hsfau.staden
-rw-r-----   1 gwilliam cs            539 Aug 10 16:09 hsfau.staden

[Doesn't make 'jjj.seq', but makes 'hsfau.staden'.]


Thanks,
Gary

-- 
Gary Williams               Tel: +44 1223 494522  Fax: +44 1223 494512
mailto:G.Williams at hgmp.mrc.ac.uk            http://www.hgmp.mrc.ac.uk/
Bioinformatics,MRC HGMP Resource Centre,Hinxton,Cambridge, CB10 1SB,UK